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Amezrou R, Ducasse A, Compain J, Lapalu N, Pitarch A, Dupont L, Confais J, Goyeau H, Kema GHJ, Croll D, Amselem J, Sanchez-Vallet A, Marcel TC. Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing. Nat Commun 2024; 15:1933. [PMID: 38431601 PMCID: PMC10908820 DOI: 10.1038/s41467-024-46191-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/14/2024] [Indexed: 03/05/2024] Open
Abstract
Knowledge of genetic determinism and evolutionary dynamics mediating host-pathogen interactions is essential to manage fungal plant diseases. Studies on the genetic architecture of fungal pathogenicity often focus on large-effect effector genes triggering strong, qualitative resistance. It is not clear how this translates to predominately quantitative interactions. Here, we use the Zymoseptoria tritici-wheat model to elucidate the genetic architecture of quantitative pathogenicity and mechanisms mediating host adaptation. With a multi-host genome-wide association study, we identify 19 high-confidence candidate genes associated with quantitative pathogenicity. Analysis of genetic diversity reveals that sequence polymorphism is the main evolutionary process mediating differences in quantitative pathogenicity, a process that is likely facilitated by genetic recombination and transposable element dynamics. Finally, we use functional approaches to confirm the role of an effector-like gene and a methyltransferase in phenotypic variation. This study highlights the complex genetic architecture of quantitative pathogenicity, extensive diversifying selection and plausible mechanisms facilitating pathogen adaptation.
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Affiliation(s)
- Reda Amezrou
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France.
| | - Aurélie Ducasse
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Jérôme Compain
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | - Anais Pitarch
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Laetitia Dupont
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Johann Confais
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | | | - Gert H J Kema
- Plant Research International B.V., Wageningen, The Netherlands
| | - Daniel Croll
- Department of Ecology and Evolution, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Joëlle Amselem
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
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2
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Degnan RM, Shuey LS, Radford-Smith J, Gardiner DM, Carroll BJ, Mitter N, McTaggart AR, Sawyer A. Double-stranded RNA prevents and cures infection by rust fungi. Commun Biol 2023; 6:1234. [PMID: 38057635 PMCID: PMC10700371 DOI: 10.1038/s42003-023-05618-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
Fungal pathogens that impact perennial plants or natural ecosystems require management strategies beyond fungicides and breeding for resistance. Rust fungi, some of the most economically and environmentally important plant pathogens, have shown amenability to double-stranded RNA (dsRNA) mediated control. To date, dsRNA treatments have been applied prior to infection or together with the inoculum. Here we show that a dsRNA spray can effectively prevent and cure infection by Austropuccinia psidii (cause of myrtle rust) at different stages of the disease cycle. Significant reductions in disease coverage were observed in plants treated with dsRNA targeting essential fungal genes 48 h pre-infection through to 14 days post-infection. For curative treatments, improvements in plant health and photosynthetic capacity were seen 2-6 weeks post-infection. Two-photon microscopy suggests inhibitory activity of dsRNA on intercellular hyphae or haustoria. Our results show that dsRNA acts both preventively and curatively against myrtle rust disease, with treated plants recovering from severe infection. These findings have immediate potential in the management of the more than 10-year epidemic of myrtle rust in Australia.
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Affiliation(s)
- Rebecca M Degnan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
| | - Louise S Shuey
- Department of Agriculture and Fisheries, Queensland Government, Ecosciences Precinct, Dutton Park, Queensland, Australia
| | - Julian Radford-Smith
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Donald M Gardiner
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, Australia
| | - Alistair R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, Australia
| | - Anne Sawyer
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, Australia.
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3
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Zhou Y, Lu X, Hao J, Li S. Quantitative Acetylome Analysis of Differentially Modified Proteins in Virulence-Differentiated Fusarium oxysporum f. sp. cucumerinum Isolates during Cucumber Colonization. J Fungi (Basel) 2023; 9:920. [PMID: 37755028 PMCID: PMC10532600 DOI: 10.3390/jof9090920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Fusarium oxysporum f. sp. cucumerinum (Foc) is a prominent pathogen that adversely affects cucumber (Cucumis sativus) production. In the pathogen's parasitic lifestyle, the pathogenesis and virulence evolution may be regulated by lysine acetylation, as demonstrated in many living organisms. However, its specific function in Foc remains poorly understood. In this study, the acetylome profiles of a mild virulence strain (foc-3b) and its derived virulence-enhanced strain (Ra-4) were analyzed before and post-inoculation on cucumber plants. In total, 10,664 acetylation sites were identified corresponding to 3874 proteins, and 45 conserved acetylation motifs were detected. Through comparison of the acetylomes, numerous differentially lysine-acetylated proteins were enriched in energy metabolism and protein processing processes, indicating the critical role of lysine acetylation during the transition from the saprotrophic lifestyle to the parasitic lifestyle. Comparative acetylome analyses on the two virulence-differentiated strains revealed that several differentially lysine-acetylated proteins were involved in pathways of defense response and energy metabolism. Ra-4 showed enhanced energy metabolism compared to foc-3b. This indicates that robust metabolic activity is required to achieve high virulence and facilitating adaptive evolution. Additionally, faster host responses are supported by an ample energy supply enhancing virulence. Thus, lysine acetylation plays a crucial role in the pathogenesis and virulence evolution of Foc.
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Affiliation(s)
- Ying Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohong Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianjun Hao
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Shidong Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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4
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Jost M, Outram MA, Dibley K, Zhang J, Luo M, Ayliffe M. Plant and pathogen genomics: essential approaches for stem rust resistance gene stacks in wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1223504. [PMID: 37727853 PMCID: PMC10505659 DOI: 10.3389/fpls.2023.1223504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/27/2023] [Indexed: 09/21/2023]
Abstract
The deployment of disease resistance genes is currently the most economical and environmentally sustainable method of crop protection. However, disease resistance genes can rapidly break down because of constant pathogen evolution, particularly when they are deployed singularly. Polygenic resistance is, therefore, considered the most durable, but combining and maintaining these genes by breeding is a laborious process as effective genes are usually unlinked. The deployment of polygenic resistance with single-locus inheritance is a promising innovation that overcomes these difficulties while enhancing resistance durability. Because of major advances in genomic technologies, increasing numbers of plant resistance genes have been cloned, enabling the development of resistance transgene stacks (RTGSs) that encode multiple genes all located at a single genetic locus. Gene stacks encoding five stem rust resistance genes have now been developed in transgenic wheat and offer both breeding simplicity and potential resistance durability. The development of similar genomic resources in phytopathogens has advanced effector gene isolation and, in some instances, enabled functional validation of individual resistance genes in RTGS. Here, the wheat stem rust pathosystem is used as an illustrative example of how host and pathogen genomic advances have been instrumental in the development of RTGS, which is a strategy applicable to many other agricultural crop species.
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Affiliation(s)
| | | | | | | | | | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
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5
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Dodds PN. From Gene-for-Gene to Resistosomes: Flor's Enduring Legacy. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:461-467. [PMID: 37697270 DOI: 10.1094/mpmi-06-23-0081-hh] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
The gene-for-gene model proposed by H. H. Flor has been one of the fundamental precepts of plant-pathogen interactions that has underpinned decades of research towards our current concepts of plant immunity. The broad validity of this model as an elegant and accurate genetic description of specific recognition events between the products of plant resistance (R) and pathogen avirulence (Avr) genes has been demonstrated many times over in a wide variety of plant disease systems. In recent years detailed molecular and structural analyses have provided a deep understanding of the principles by which plant immune receptors recognize pathogen effectors, including providing molecular descriptions of many of the genetic loci in flax and flax rust characterized by Flor. Recent advances in molecular and structural understanding of immune receptor recognition and activation mechanisms have brought the field to a new level, where rational design of novel receptors through engineering approaches is becoming a realizable goal. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Peter N Dodds
- CSIRO Agriculture and Food, GPO Box 1700, Clunies Ross Street, Canberra 2601, Australia
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6
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Guo Y, Betzen B, Salcedo A, He F, Bowden RL, Fellers JP, Jordan KW, Akhunova A, Rouse MN, Szabo LJ, Akhunov E. Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races. Nat Commun 2022; 13:6287. [PMID: 36271077 PMCID: PMC9587050 DOI: 10.1038/s41467-022-34050-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe yield losses. The factors driving the evolution of its virulence and adaptation remain poorly characterized. We utilize long-read sequencing to develop a haplotype-resolved genome assembly of a U.S. isolate of Pgt. Using Pgt haplotypes as a reference, we characterize the structural variants (SVs) and single nucleotide polymorphisms in a diverse panel of isolates. SVs impact the repertoire of predicted effectors, secreted proteins involved in host-pathogen interaction, and show evidence of purifying selection. By analyzing global and local genomic ancestry we demonstrate that the origin of 8 out of 12 Pgt clades is linked with either somatic hybridization or sexual recombination between the diverged donor populations. Our study shows that SVs and admixture events appear to play an important role in broadening Pgt virulence and the origin of highly virulent races, creating a resource for studying the evolution of Pgt virulence and preventing future epidemic outbreaks.
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Affiliation(s)
- Yuanwen Guo
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA
| | - Bliss Betzen
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Present Address: USDA-APHIS-PPQ Field Operations, Kansas State University, Manhattan, KS USA
| | - Andres Salcedo
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.40803.3f0000 0001 2173 6074Present Address: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Fei He
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.9227.e0000000119573309Present Address: State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Robert L. Bowden
- grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - John P. Fellers
- grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - Katherine W. Jordan
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - Alina Akhunova
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Integrated Genomics Facility, Kansas State University, Manhattan, KS USA
| | - Mathew N. Rouse
- grid.512864.c0000 0000 8881 3436Department of Plant Pathology, University of Minnesota & USDA-ARS, Cereal Disease Lab, St. Paul, MN USA
| | - Les J. Szabo
- grid.512864.c0000 0000 8881 3436Department of Plant Pathology, University of Minnesota & USDA-ARS, Cereal Disease Lab, St. Paul, MN USA
| | - Eduard Akhunov
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Wheat Genetics Resource Center, Kansas State University, Manhattan, KS USA
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7
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Skiadas P, Klein J, Quiroz Monnens T, Elberse J, de Jonge R, Van den Ackerveken G, Seidl MF. Sexual reproduction contributes to the evolution of resistance breaking isolates of the spinach pathogen Peronospora effusa. Environ Microbiol 2022; 24:1622-1637. [PMID: 35191594 PMCID: PMC9304176 DOI: 10.1111/1462-2920.15944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
Peronospora effusa causes downy mildew, the economically most important disease of cultivated spinach worldwide. To date, 19 P. effusa races have been denominated based on their capacity to break spinach resistances, but their genetic diversity and the evolutionary processes that contribute to race emergence are unknown. Here, we performed the first systematic analysis of P. effusa races showing that those emerge by both asexual and sexual reproduction. Specifically, we studied the diversity of 26 P. effusa isolates from 16 denominated races based on mitochondrial and nuclear comparative genomics. Mitochondrial genomes based on long‐read sequencing coupled with diversity assessment based on short‐read sequencing uncovered two mitochondrial haplogroups, each with distinct genome organization. Nuclear genome‐wide comparisons of the 26 isolates revealed that 10 isolates from six races could clearly be divided into three asexually evolving groups, in concordance with their mitochondrial phylogeny. The remaining isolates showed signals of reticulated evolution and discordance between nuclear and mitochondrial phylogenies, suggesting that these evolved through sexual reproduction. Increased understanding of this pathogen's reproductive modes will provide the framework for future studies into the molecular mechanisms underlying race emergence and into the P. effusa‐spinach interaction, thus assisting in sustainable production of spinach through knowledge‐driven resistance breeding.
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Affiliation(s)
- Petros Skiadas
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584, CH, Utrecht, The Netherlands.,Plant-Microbe Interactions, Utrecht University, Padualaan 8 3584 CH, Utrecht, The Netherlands
| | - Joël Klein
- Plant-Microbe Interactions, Utrecht University, Padualaan 8 3584 CH, Utrecht, The Netherlands
| | - Thomas Quiroz Monnens
- Plant-Microbe Interactions, Utrecht University, Padualaan 8 3584 CH, Utrecht, The Netherlands
| | - Joyce Elberse
- Plant-Microbe Interactions, Utrecht University, Padualaan 8 3584 CH, Utrecht, The Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Utrecht University, Padualaan 8 3584 CH, Utrecht, The Netherlands
| | | | - Michael F Seidl
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584, CH, Utrecht, The Netherlands
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8
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Matsvay A, Dyachkova M, Mikhaylov I, Kiselev D, Say A, Burskaia V, Artyushin I, Khafizov K, Shipulin G. Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus. Microorganisms 2021; 10:31. [PMID: 35056480 PMCID: PMC8781740 DOI: 10.3390/microorganisms10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/03/2023] Open
Abstract
Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host's ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.
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Affiliation(s)
- Alina Matsvay
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - Marina Dyachkova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Ivan Mikhaylov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Daniil Kiselev
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, 34091 Montpellier, France
| | - Anna Say
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | | | - Ilya Artyushin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
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9
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Wang YP, Pan ZC, Yang LN, Burdon JJ, Friberg H, Sui QJ, Zhan J. Optimizing Plant Disease Management in Agricultural Ecosystems Through Rational In-Crop Diversification. FRONTIERS IN PLANT SCIENCE 2021; 12:767209. [PMID: 35003160 PMCID: PMC8739928 DOI: 10.3389/fpls.2021.767209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Biodiversity plays multifaceted roles in societal development and ecological sustainability. In agricultural ecosystems, using biodiversity to mitigate plant diseases has received renewed attention in recent years but our knowledge of the best ways of using biodiversity to control plant diseases is still incomplete. In term of in-crop diversification, it is not clear how genetic diversity per se in host populations interacts with identifiable resistance and other functional traits of component genotypes to mitigate disease epidemics and what is the best way of structuring mixture populations. In this study, we created a series of host populations by mixing different numbers of potato varieties showing different late blight resistance levels in different proportions. The amount of naturally occurring late blight disease in the mixture populations was recorded weekly during the potato growing seasons. The percentage of disease reduction (PDR) in the mixture populations was calculated by comparing their observed late blight levels relative to that expected when they were planted in pure stands. We found that PDR in the mixtures increased as the number of varieties and the difference in host resistance (DHR) between the component varieties increased. However, the level of host resistance in the potato varieties had little impact on PDR. In mixtures involving two varieties, the optimum proportion of component varieties for the best PDR depended on their DHR, with an increasing skewness to one of the component varieties as the DHR between the component varieties increased. These results indicate that mixing crop varieties can significantly reduce disease epidemics in the field. To achieve the best disease mitigation, growers should include as many varieties as possible in mixtures or, if only two component mixtures are possible, increase DHR among the component varieties.
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Affiliation(s)
- Yan-Ping Wang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Zhe-Chao Pan
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Li-Na Yang
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | | | - Hanna Friberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Qi-jun Sui
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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10
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Stephens C, Ölmez F, Blyth H, McDonald M, Bansal A, Turgay EB, Hahn F, Saintenac C, Nekrasov V, Solomon P, Milgate A, Fraaije B, Rudd J, Kanyuka K. Remarkable recent changes in the genetic diversity of the avirulence gene AvrStb6 in global populations of the wheat pathogen Zymoseptoria tritici. MOLECULAR PLANT PATHOLOGY 2021; 22:1121-1133. [PMID: 34258838 PMCID: PMC8358995 DOI: 10.1111/mpp.13101] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 04/02/2021] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is one of the most economically important diseases of wheat. Recently, both factors of a gene-for-gene interaction between Z. tritici and wheat, the wheat receptor-like kinase Stb6 and the Z. tritici secreted effector protein AvrStb6, have been identified. Previous analyses revealed a high diversity of AvrStb6 haplotypes present in earlier Z. tritici isolate collections, with up to c.18% of analysed isolates possessing the avirulence isoform of AvrStb6 identical to that originally identified in the reference isolate IPO323. With Stb6 present in many commercial wheat cultivars globally, we aimed to assess potential changes in AvrStb6 genetic diversity and the incidence of haplotypes allowing evasion of Stb6-mediated resistance in more recent Z. tritici populations. Here we show, using targeted resequencing of AvrStb6, that this gene is universally present in field isolates sampled from major wheat-growing regions of the world in 2013-2017. However, in contrast to the data from previous AvrStb6 population studies, we report a complete absence of the originally described avirulence isoform of AvrStb6 amongst modern Z. tritici isolates. Moreover, a remarkably small number of haplotypes, each encoding AvrStb6 protein isoforms conditioning virulence on Stb6-containing wheat, were found to predominate among modern Z. tritici isolates. A single virulence isoform of AvrStb6 was found to be particularly abundant throughout the global population. These findings indicate that, despite the ability of Z. tritici to sexually reproduce on resistant hosts, AvrStb6 avirulence haplotypes tend to be eliminated in subsequent populations.
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Affiliation(s)
| | - Fatih Ölmez
- Department of Plant ProtectionSivas Science and Technology UniversitySivasTurkey
| | - Hannah Blyth
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
| | - Megan McDonald
- Division of Plant SciencesResearch School of BiologyAustralian National UniversityCanberraAustralia
- Present address:
Megan McDonald, School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Anuradha Bansal
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
- Present address:
British American TobaccoSouthamptonUK
| | - Emine Burcu Turgay
- Department of Plant PathologyPlant Protection Central Research InstituteField Crops Central Research InstituteAnkaraTurkey
| | - Florian Hahn
- Department of Plant SciencesRothamsted ResearchHarpendenUK
- Present address:
Department of Plant SciencesUniversity of OxfordOxfordUK
| | | | | | - Peter Solomon
- Division of Plant SciencesResearch School of BiologyAustralian National UniversityCanberraAustralia
| | - Andrew Milgate
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaAustralia
| | - Bart Fraaije
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
- Present address:
NIABCambridgeUK
| | - Jason Rudd
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
| | - Kostya Kanyuka
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
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11
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Duplessis S, Lorrain C, Petre B, Figueroa M, Dodds PN, Aime MC. Host Adaptation and Virulence in Heteroecious Rust Fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:403-422. [PMID: 34077239 DOI: 10.1146/annurev-phyto-020620-121149] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rust fungi (Pucciniales, Basidiomycota) are obligate biotrophic pathogens that cause rust diseases in plants, inflicting severe damage to agricultural crops. Pucciniales possess the most complex life cycles known in fungi. These include an alternation of generations, the development of up to five different sporulating stages, and, for many species, the requirement of infecting two unrelated host plants during different parts of their life cycle, termed heteroecism. These fungi have been extensively studied in the past century through microscopy and inoculation studies, providing precise descriptions of their infection processes, although the molecular mechanisms underlying their unique biology are poorly understood. In this review, we cover recent genomic and life cycle transcriptomic studies in several heteroecious rust species, which provide insights into the genetic tool kits associated with host adaptation and virulence, opening new avenues for unraveling their unique evolution.
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Affiliation(s)
- Sebastien Duplessis
- Université de Lorraine, INRAE, UMR 1136 IAM, Interactions Arbres-Microorganismes, 54000 Nancy, France; ,
| | - Cecile Lorrain
- Plant Pathology Group, ETH Zurich, 8092 Zurich, Switzerland;
| | - Benjamin Petre
- Université de Lorraine, INRAE, UMR 1136 IAM, Interactions Arbres-Microorganismes, 54000 Nancy, France; ,
| | - Melania Figueroa
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia; ,
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia; ,
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA;
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12
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Leaping into the Unknown World of Sporisorium scitamineum Candidate Effectors. J Fungi (Basel) 2020; 6:jof6040339. [PMID: 33291820 PMCID: PMC7762069 DOI: 10.3390/jof6040339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
Sporisorium scitamineum is a biotrophic fungus causing sugarcane smut disease. In this study, we set up a pipeline and used genomic and dual transcriptomic data previously obtained by our group to identify candidate effectors of S. scitamineum and their expression profiles in infected smut-resistant and susceptible sugarcane plants. The expression profile of different genes after infection in contrasting sugarcane genotypes assessed by RT-qPCR depended on the plant genotypes and disease progression. Three candidate effector genes expressed earlier only in resistant plants, four expressed in both genotypes, and three later in susceptible plants. Ten genes were cloned and transiently expressed in N. benthamiana leaves to determine their subcellular location, while four localized in more than one compartment. Two candidates, g3890 having a nucleoplasmic and mitochondrial location and g5159 targeting the plant cell wall, were selected to obtain their possible corresponding host targets using co-immunoprecipitation (CoIP) experiments and mass spectrometry. Various potential interactors were identified, including subunits of the protein phosphatase 2A and an endochitinase. We investigated the presence of orthologs in sugarcane and using transcriptome data present their expression profiles. Orthologs of sugarcane shared around 70% similarity. Identifying a set of putative fungal effectors and their plant targets provides a valuable resource for functional characterization of the molecular events leading to smut resistance in sugarcane plants and uncovers further opportunities for investigation.
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13
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Miller ME, Nazareno ES, Rottschaefer SM, Riddle J, Dos Santos Pereira D, Li F, Nguyen-Phuc H, Henningsen EC, Persoons A, Saunders DGO, Stukenbrock E, Dodds PN, Kianian SF, Figueroa M. Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci. PLoS Genet 2020; 16:e1009291. [PMID: 33370783 PMCID: PMC7793281 DOI: 10.1371/journal.pgen.1009291] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 01/08/2021] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Pathogen populations are expected to evolve virulence traits in response to resistance deployed in agricultural settings. However, few temporal datasets have been available to characterize this process at the population level. Here, we examined two temporally separated populations of Puccinia coronata f. sp. avenae (Pca), which causes crown rust disease in oat (Avena sativa) sampled from 1990 to 2015. We show that a substantial increase in virulence occurred from 1990 to 2015 and this was associated with a genetic differentiation between populations detected by genome-wide sequencing. We found strong evidence for genetic recombination in these populations, showing the importance of the alternate host in generating genotypic variation through sexual reproduction. However, asexual expansion of some clonal lineages was also observed within years. Genome-wide association analysis identified seven Avr loci associated with virulence towards fifteen Pc resistance genes in oat and suggests that some groups of Pc genes recognize the same pathogen effectors. The temporal shift in virulence patterns in the Pca populations between 1990 and 2015 is associated with changes in allele frequency in these genomic regions. Nucleotide diversity patterns at a single Avr locus corresponding to Pc38, Pc39, Pc55, Pc63, Pc70, and Pc71 showed evidence of a selective sweep associated with the shift to virulence towards these resistance genes in all 2015 collected isolates.
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Affiliation(s)
- Marisa E. Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric S. Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Susan M. Rottschaefer
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Jakob Riddle
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Danilo Dos Santos Pereira
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plon, Germany
- Christian-Albrechts University of Kiel, Kiel Germany
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Hoa Nguyen-Phuc
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eva C. Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Antoine Persoons
- INRA/Universite de Lorraine Interactions Abres/Microorganismes, Champenoux, France
| | | | - Eva Stukenbrock
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plon, Germany
- Christian-Albrechts University of Kiel, Kiel Germany
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia
| | - Shahryar F. Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia
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14
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Korfanty G, Stanley K, Lammers K, Fan Y, Xu J. Variations in sexual fitness among natural strains of the opportunistic human fungal pathogen Aspergillus fumigatus. INFECTION GENETICS AND EVOLUTION 2020; 87:104640. [PMID: 33246083 DOI: 10.1016/j.meegid.2020.104640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 10/05/2020] [Accepted: 11/21/2020] [Indexed: 10/22/2022]
Abstract
Aspergillus fumigatus is a ubiquitous ascomycete fungus, naturally inhabiting the soil and compost piles. Its conidia readily disperse into the atmosphere and cause opportunistic infections known as aspergillosis. With the emerging resistance to many antifungal drugs, our understanding of A. fumigatus epidemiology has become increasingly important for developing effective control and treatment strategies. As a pathogen capable of both sexual and asexual reproduction, mutations causing drug resistance and increased virulence could be spread rapidly in A. fumigatus populations. However, relatively little is known about the distributions of sexual reproductive fitness among natural strains of A. fumigatus. Here we investigated the formation of sexual reproductive structure (i.e. cleistothecia) and sexual spore viability among 60 natural strains of A. fumigatus. These strains were from six geographically distant countries (India, China, Canada, Cameroon, Saudi Arabia, and New Zealand), with 10 strains (including five MAT1-1 strains and five MAT1-2 strains) from each country. These strains were crossed in all combinations with strains of the opposite mating type. In addition, all 60 strains were crossed with either AFB62-1 (MAT1-1) or AFIR928 (MAT1-2), two reference supermater strains. Of the 900 crosses among the 60 natural strains, 136 crosses (15.1%) produced cleistothecia. Our analyses revealed that strains from China had the highest average ability to form cleistothecia, followed by those from New Zealand, Saudi Arabia, India, Canada, and Cameroon. Among the crosses that produced cleistothecia, about 40% produced viable ascospores, with the rate of ascospore germination varied significantly among crosses. Interestingly, neither the ability to form cleistothecia nor ascospore germination rate showed any distinct relationships with either geographic or genetic distance between parental strains. Our results suggest that genetic exchange among geographically and genetically divergent strains of A. fumigatus are possible. However, the rates of genetic exchange likely vary among strains and populations in nature.
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Affiliation(s)
- Greg Korfanty
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Kaitlin Stanley
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Kaitlyn Lammers
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - YuYing Fan
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada.
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15
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Li J, Cornelissen B, Rep M. Host-specificity factors in plant pathogenic fungi. Fungal Genet Biol 2020; 144:103447. [PMID: 32827756 DOI: 10.1016/j.fgb.2020.103447] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 01/18/2023]
Abstract
Fortunately, no fungus can cause disease on all plant species, and although some plant-pathogenic fungi have quite a broad host range, most are highly limited in the range of plant species or even cultivars that they cause disease in. The mechanisms of host specificity have been extensively studied in many plant-pathogenic fungi, especially in fungal pathogens causing disease on economically important crops. Specifically, genes involved in host specificity have been identified during the last few decades. In this overview, we describe and discuss these host-specificity genes. These genes encode avirulence (Avr) proteins, proteinaceous host-specific toxins or secondary metabolites. We discuss the genomic context of these genes, their expression, polymorphism, horizontal transfer and involvement in pathogenesis.
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Affiliation(s)
- Jiming Li
- Molecular Plant Pathology, University of Amsterdam, Amsterdam 1098 XH, the Netherlands
| | - Ben Cornelissen
- Molecular Plant Pathology, University of Amsterdam, Amsterdam 1098 XH, the Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, University of Amsterdam, Amsterdam 1098 XH, the Netherlands.
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16
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Susi H, Burdon JJ, Thrall PH, Nemri A, Barrett LG. Genetic analysis reveals long-standing population differentiation and high diversity in the rust pathogen Melampsora lini. PLoS Pathog 2020; 16:e1008731. [PMID: 32810177 PMCID: PMC7454959 DOI: 10.1371/journal.ppat.1008731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/28/2020] [Accepted: 06/22/2020] [Indexed: 11/18/2022] Open
Abstract
A priority for research on infectious disease is to understand how epidemiological and evolutionary processes interact to influence pathogen population dynamics and disease outcomes. However, little is understood about how population adaptation changes across time, how sexual vs. asexual reproduction contribute to the spread of pathogens in wild populations and how diversity measured with neutral and selectively important markers correlates across years. Here, we report results from a long-term study of epidemiological and genetic dynamics within several natural populations of the Linum marginale-Melampsora lini plant-pathogen interaction. Using pathogen isolates collected from three populations of wild flax (L. marginale) spanning 16 annual epidemics, we probe links between pathogen population dynamics, phenotypic variation for infectivity and genomic polymorphism. Pathogen genotyping was performed using 1567 genome-wide SNP loci and sequence data from two infectivity loci (AvrP123, AvrP4). Pathogen isolates were phenotyped for infectivity using a differential set. Patterns of epidemic development were assessed by conducting surveys of infection prevalence in one population (Kiandra) annually. Bayesian clustering analyses revealed host population and ecotype as key predictors of pathogen genetic structure. Despite strong fluctuations in pathogen population size and severe annual bottlenecks, analysis of molecular variance revealed that pathogen population differentiation was relatively stable over time. Annually, varying levels of clonal spread (0–44.8%) contributed to epidemics. However, within populations, temporal genetic composition was dynamic with rapid turnover of pathogen genotypes, despite the dominance of only four infectivity phenotypes across the entire study period. Furthermore, in the presence of strong fluctuations in population size and migration, spatial selection may maintain pathogen populations that, despite being phenotypically stable, are genetically highly dynamic. Melampsora lini is a rust fungus that infects native flax, Linum marginale in south-eastern Australia where its epidemiology and evolution have been intensively studied since 1987. Over that time, substantial diversity in the pathotypic structure of M. lini has been demonstrated but an understanding of how genetic diversity in pathogen populations is maintained through space and time is lacking. Here we integrated phenotypic, genotypic and epidemiological datasets spanning 16 annual epidemics across three host populations to examine long-term pathogen genetic dynamics. The results show that host ecotype is the dominant selective force in the face of strong bottlenecks and annual patterns of genetic turnover. Results from previous studies indicate that in this geographic region, M. lini lacks the capacity to reproduce sexually–we thus expected to find limited genetic diversity and evidence for strong clonality influencing genetic dynamics within growing seasons. However, the breadth of genomic coverage provided by the SNP markers revealed high levels of genotypic variation within M. lini populations. This discovery contrasts with observed phenotypic dynamics as the epidemics of this pathogen were largely dominated by four pathotypes across the study period. Based on a detailed assessment and comparison of pathotypic and genotypic patterns, our study increases the understanding of how genetic diversity is generated and maintained through space and time within wild pathogen populations. The implications for the management of resistance to pathogens in agricultural or conservation contexts are significant: the appearance of clonality may be hiding high levels of pathogen diversity and recombination. Understanding how this diversity is generated could provide new and unique ways to mitigate or suppress the emergence of infectious strains, allowing to efficiently combat harmful diseases.
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Affiliation(s)
- Hanna Susi
- CSIRO Agriculture & Food, Canberra, Australia
- * E-mail:
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17
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Karasov TL, Shirsekar G, Schwab R, Weigel D. What natural variation can teach us about resistance durability. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:89-98. [PMID: 32535454 DOI: 10.1016/j.pbi.2020.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/08/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
Breeding a crop variety to be resistant to a pathogen usually takes years. This is problematic because pathogens, with short generation times and fluid genomes, adapt quickly to overcome resistance. The triumph of the pathogen is not inevitable, however, as there are numerous examples of durable resistance, particularly in wild plants. Which factors then contribute to such resistance stability over millennia? We review current knowledge of wild and agricultural pathosystems, detailing the importance of genetic, species and spatial heterogeneity in the prevention of pathogen outbreaks. We also highlight challenges associated with increasing resistance diversity in crops, both in light of pathogen (co-)evolution and breeding practices. Historically it has been difficult to incorporate heterogeneity into agriculture due to reduced efficiency in harvesting. Recent advances implementing computer vision and automation in agricultural production may improve our ability to harvest mixed genotype and mixed species plantings, thereby increasing resistance durability.
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Affiliation(s)
- Talia L Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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18
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Figueroa M, Dodds PN, Henningsen EC. Evolution of virulence in rust fungi - multiple solutions to one problem. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:20-27. [PMID: 32244171 DOI: 10.1016/j.pbi.2020.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 05/18/2023]
Abstract
Rust fungi are major pathogens that negatively affect crops and ecosystems. Recent rust disease epidemics driven by the emergence of strains with novel virulence profiles demand a better understanding of the evolutionary mechanisms of these organisms. Here, we review research advances in genome-scale analysis coupled with functional validation of effector candidate genes that have been instrumental to elucidate processes that contribute to changes in virulence phenotypes. We highlight how haplotype-phased genome references have paved the road to link these processes to the reproductive phases of rust fungi and have provided evidence for somatic exchange between strains as an important mechanism for generating diversity in asexual populations. With increasing data availability, we envision the future development of molecular virulence diagnostic tools.
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Affiliation(s)
- Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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19
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Munir S, Li Y, He P, Huang M, He P, He P, Cui W, Wu Y, He Y. Core endophyte communities of different citrus varieties from citrus growing regions in China. Sci Rep 2020; 10:3648. [PMID: 32108149 PMCID: PMC7046616 DOI: 10.1038/s41598-020-60350-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 02/11/2020] [Indexed: 02/07/2023] Open
Abstract
The native microbiomes of citrus trees play important roles in plant health, with good communication between the native microbiome and the host plant. Here, we report on the native endophytes in 24 citrus varieties in nine citrus growing regions in China; some of the trees were healthy and others had asymptomatic or symptomatic huanglongbing, which is caused by the pathogen Candidatus Liberibacter asiaticus (CLas). We used culture-dependent analysis and characterized the isolates by partial 16S rRNA gene sequencing. The endophytes were compared between different citrus varieties, regions, and disease states (healthy, asymptomatic, and symptomatic). The total number of endophytes isolated from most of the citrus varieties was 104-106 CFU/g of leaves, but it differed significantly by disease state, with the highest numbers in the healthy leaves and the lowest in the symptomatic leaves (p < 0.05). Among the citrus varieties, the Valencia variety had the maximum number of endophyte species (22). The most dominant endophytes were Bacillus subtilis, B. velezensis, Curtobacterium luteum, and Microbacterium testaceum. The higher frequency of B. subtilis in the healthy/asymptomatic plants compared to the symptomatic plants suggests that it has a role in huanglongbing resistance. Native endophyte communities in various citrus varieties could be used to improve citrus growth and combat CLas.
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Affiliation(s)
- Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yongmei Li
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Min Huang
- Agriculture College and Urban Modern Agriculture Engineering Research Center, Kunming University, Kunming, 650214, Yunnan, China
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Pengjie He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Wenyan Cui
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yixin Wu
- National and Local Joint Engineering Research Center for Screening and Application of Microbial Strains, Kunming, 650217, Yunnan, China
- Faculty of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
- National and Local Joint Engineering Research Center for Screening and Application of Microbial Strains, Kunming, 650217, Yunnan, China.
- Faculty of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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20
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Wu W, Nemri A, Blackman LM, Catanzariti AM, Sperschneider J, Lawrence GJ, Dodds PN, Jones DA, Hardham AR. Flax rust infection transcriptomics reveals a transcriptional profile that may be indicative for rust Avr genes. PLoS One 2019; 14:e0226106. [PMID: 31830116 PMCID: PMC6907798 DOI: 10.1371/journal.pone.0226106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/19/2019] [Indexed: 01/04/2023] Open
Abstract
Secreted effectors of fungal pathogens are essential elements for disease development. However, lack of sequence conservation among identified effectors has long been a problem for predicting effector complements in fungi. Here we have explored the expression characteristics of avirulence (Avr) genes and candidate effectors of the flax rust fungus, Melampsora lini. We performed transcriptome sequencing and real-time quantitative PCR (qPCR) on RNA extracted from ungerminated spores, germinated spores, isolated haustoria and flax seedlings inoculated with M. lini isolate CH5 during plant infection. Genes encoding two categories of M. lini proteins, namely Avr proteins and plant cell wall degrading enzymes (CWDEs), were investigated in detail. Analysis of the expression profiles of 623 genes encoding predicted secreted proteins in the M. lini transcriptome shows that the six known Avr genes (i.e. AvrM (avrM), AvrM14, AvrL2, AvrL567, AvrP123 (AvrP) and AvrP4) fall within a group of 64 similarly expressed genes that are induced in planta and show a peak of expression early in infection with a subsequent decline towards sporulation. Other genes within this group include two paralogues of AvrL2, an AvrL567 virulence allele, and a number of genes encoding putative effector proteins. By contrast, M. lini genes encoding CWDEs fall into different expression clusters with their distribution often unrelated to their catalytic activity or substrate targets. These results suggest that synthesis of M. lini Avr proteins may be regulated in a coordinated fashion and that the expression profiling-based analysis has significant predictive power for the identification of candidate Avr genes.
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Affiliation(s)
- Wenjie Wu
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
- * E-mail:
| | | | - Leila M. Blackman
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Ann-Maree Catanzariti
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, the Australian National University, Canberra, Australia
| | | | | | - David A. Jones
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Adrienne R. Hardham
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
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21
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de Guillen K, Lorrain C, Tsan P, Barthe P, Petre B, Saveleva N, Rouhier N, Duplessis S, Padilla A, Hecker A. Structural genomics applied to the rust fungus Melampsora larici-populina reveals two candidate effector proteins adopting cystine knot and NTF2-like protein folds. Sci Rep 2019; 9:18084. [PMID: 31792250 PMCID: PMC6889267 DOI: 10.1038/s41598-019-53816-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/31/2019] [Indexed: 12/29/2022] Open
Abstract
Rust fungi are plant pathogens that secrete an arsenal of effector proteins interfering with plant functions and promoting parasitic infection. Effectors are often species-specific, evolve rapidly, and display low sequence similarities with known proteins. How rust fungal effectors function in host cells remains elusive, and biochemical and structural approaches have been scarcely used to tackle this question. In this study, we produced recombinant proteins of eleven candidate effectors of the leaf rust fungus Melampsora larici-populina in Escherichia coli. We successfully purified and solved the three-dimensional structure of two proteins, MLP124266 and MLP124017, using NMR spectroscopy. Although both MLP124266 and MLP124017 show no sequence similarity with known proteins, they exhibit structural similarities to knottins, which are disulfide-rich small proteins characterized by intricate disulfide bridges, and to nuclear transport factor 2-like proteins, which are molecular containers involved in a wide range of functions, respectively. Interestingly, such structural folds have not been reported so far in pathogen effectors, indicating that MLP124266 and MLP124017 may bear novel functions related to pathogenicity. Our findings show that sequence-unrelated effectors can adopt folds similar to known proteins, and encourage the use of biochemical and structural approaches to functionally characterize effector candidates.
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Affiliation(s)
- Karine de Guillen
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR 5048, Univ Montpellier, F-34090, Montpellier, France
| | - Cécile Lorrain
- Université de Lorraine, INRA, IAM, F-54000, Nancy, France
| | - Pascale Tsan
- Université de Lorraine, CNRS, CRM2, F-54000, Nancy, France
| | - Philippe Barthe
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR 5048, Univ Montpellier, F-34090, Montpellier, France
| | - Benjamin Petre
- Université de Lorraine, INRA, IAM, F-54000, Nancy, France
| | | | | | | | - André Padilla
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR 5048, Univ Montpellier, F-34090, Montpellier, France
| | - Arnaud Hecker
- Université de Lorraine, INRA, IAM, F-54000, Nancy, France.
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22
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Dyachkova MS, Chekalin EV, Danilenko VN. Positive Selection in Bifidobacterium Genes Drives Species-Specific Host-Bacteria Communication. Front Microbiol 2019; 10:2374. [PMID: 31681231 PMCID: PMC6803598 DOI: 10.3389/fmicb.2019.02374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022] Open
Abstract
Bifidobacteria are commensal microorganisms that inhabit a wide range of hosts, including insects, birds and mammals. The mechanisms responsible for the adaptation of bifidobacteria to various hosts during the evolutionary process remain poorly understood. Previously, we reported that the species-specific PFNA gene cluster is present in the genomes of various species of the Bifidobacterium genus. The cluster contains signal transduction and adhesion genes that are presumably involved in the communication between bifidobacteria and their hosts. The genes in the PFNA cluster show high sequence divergence between bifidobacterial species, which may be indicative of rapid evolution that drives species-specific adaptation to the host organism. We used the maximum likelihood approach to detect positive selection in the PFNA genes. We tested for both pervasive and episodic positive selection to identify codons that experienced adaptive evolution in all and individual branches of the Bifidobacterium phylogenetic tree, respectively. Our results provide evidence that episodic positive selection has played an important role in the divergence process and molecular evolution of sequences of the species-specific PFNA genes in most bifidobacterial species. Moreover, we found the signatures of pervasive positive selection in the molecular evolution of the tgm gene in all branches of the Bifidobacterium phylogenetic tree. These results are consistent with the suggested role of PFNA gene cluster in the process of specific adaptation of bifidobacterial species to various hosts.
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Affiliation(s)
- Marina S Dyachkova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny V Chekalin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Valery N Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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23
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Richards JK, Stukenbrock EH, Carpenter J, Liu Z, Cowger C, Faris JD, Friesen TL. Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States. PLoS Genet 2019; 15:e1008223. [PMID: 31626626 PMCID: PMC6821140 DOI: 10.1371/journal.pgen.1008223] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/30/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022] Open
Abstract
Filamentous fungi rapidly evolve in response to environmental selection pressures in part due to their genomic plasticity. Parastagonospora nodorum, a fungal pathogen of wheat and causal agent of septoria nodorum blotch, responds to selection pressure exerted by its host, influencing the gain, loss, or functional diversification of virulence determinants, known as effector genes. Whole genome resequencing of 197 P. nodorum isolates collected from spring, durum, and winter wheat production regions of the United States enabled the examination of effector diversity and genomic regions under selection specific to geographically discrete populations. 1,026,859 SNPs/InDels were used to identify novel loci, as well as SnToxA and SnTox3 as factors in disease. Genes displaying presence/absence variation, predicted effector genes, and genes localized on an accessory chromosome had significantly higher pN/pS ratios, indicating a higher rate of sequence evolution. Population structure analyses indicated two P. nodorum populations corresponding to the Upper Midwest (Population 1) and Southern/Eastern United States (Population 2). Prevalence of SnToxA varied greatly between the two populations which correlated with presence of the host sensitivity gene Tsn1 in the most prevalent cultivars in the corresponding regions. Additionally, 12 and 5 candidate effector genes were observed to be under diversifying selection among isolates from Population 1 and 2, respectively, but under purifying selection or neutrally evolving in the opposite population. Selective sweep analysis revealed 10 and 19 regions that had recently undergone positive selection in Population 1 and 2, respectively, involving 92 genes in total. When comparing genes with and without presence/absence variation, those genes exhibiting this variation were significantly closer to transposable elements. Taken together, these results indicate that P. nodorum is rapidly adapting to distinct selection pressures unique to spring and winter wheat production regions by rapid adaptive evolution and various routes of genomic diversification, potentially facilitated through transposable element activity.
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Affiliation(s)
- Jonathan K. Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
| | - Eva H. Stukenbrock
- Department of Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jessica Carpenter
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Christina Cowger
- Plant Science Research Unit, USDA-ARS, Raleigh, North Carolina, United States of America
| | - Justin D. Faris
- Cereal Crops Research Unit, Edward T. Schaefer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
| | - Timothy L. Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
- Cereal Crops Research Unit, Edward T. Schaefer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
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Lorrain C, Gonçalves Dos Santos KC, Germain H, Hecker A, Duplessis S. Advances in understanding obligate biotrophy in rust fungi. THE NEW PHYTOLOGIST 2019; 222:1190-1206. [PMID: 30554421 DOI: 10.1111/nph.15641] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/13/2018] [Indexed: 05/18/2023]
Abstract
Contents Summary 1190 I. Introduction 1190 II. Rust fungi: a diverse and serious threat to agriculture 1191 III. The different facets of rust life cycles and unresolved questions about their evolution 1191 IV. The biology of rust infection 1192 V. Rusts in the genomics era: the ever-expanding list of candidate effector genes 1195 VI. Functional characterization of rust effectors 1197 VII. Putting rusts to sleep: Pucciniales research outlooks 1201 Acknowledgements 1202 References 1202 SUMMARY: Rust fungi (Pucciniales) are the largest group of plant pathogens and represent one of the most devastating threats to agricultural crops worldwide. Despite the economic importance of these highly specialized pathogens, many aspects of their biology remain obscure, largely because rust fungi are obligate biotrophs. The rise of genomics and advances in high-throughput sequencing technology have presented new options for identifying candidate effector genes involved in pathogenicity mechanisms of rust fungi. Transcriptome analysis and integrated bioinformatics tools have led to the identification of key genetic determinants of host susceptibility to infection by rusts. Thousands of genes encoding secreted proteins highly expressed during host infection have been reported for different rust species, which represents significant potential towards understanding rust effector function. Recent high-throughput in planta expression screen approaches (effectoromics) have pushed the field ahead even further towards predicting high-priority effectors and identifying avirulence genes. These new insights into rust effector biology promise to inform future research and spur the development of effective and sustainable strategies for managing rust diseases.
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Affiliation(s)
- Cécile Lorrain
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | | | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Quebec à Trois-Rivières, Trois-Rivières, QC, G9A 5H7, Canada
| | - Arnaud Hecker
- Université de Lorraine, UMR 1136 Université de Lorraine/INRA Interactions Arbres/Microorganismes, Vandoeuvre-lès-Nancy, France
| | - Sébastien Duplessis
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
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Gladieux P. What makes a specialized endophyte special? Mol Ecol 2019; 27:3037-3039. [PMID: 30133874 DOI: 10.1111/mec.14775] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/08/2018] [Indexed: 02/05/2023]
Abstract
Fungal plant symbionts can be highly specialized on a limited range of host genotypes and species. Understanding the genetic basis of this specialization, the mechanisms governing its establishment and the relationship between specialization and speciation is a major challenge for evolutionary biologists (Timms & Read, ). A deeper knowledge of evolutionary plant-microbe interactions could be exploited to improve agricultural management, by bringing fungal biodiversity and fungal biomass under greater and more durable human control. Previous studies on pathogens have shown that effectors, that is, small secreted proteins that modulate plant physiology to favour host colonization, play a key role in infection of novel hosts (e.g., Inoue et al., ) or in host specialization (e.g., Liao et al. ()). Like pathogens, endophytes also manipulate the physiology of their hosts and colonize novel hosts to which they specialize (Hardoim et al., ). These biological characteristics of endophytes raise the question of similarities in the protein arsenal contributing to the specialization of pathogens and endophytes. In this issue of Molecular Ecology, Schirrmann et al. () used a combination of divergence genome scans and tests for positive selection to investigate the genetic basis of specialization of two subspecies of the symbiont Epichloë typhina occurring on two different grass hosts. Their analyses suggest a key role of effectors as determinants of host specialization. This study paves the way towards the comparative analysis of the genomics of speciation among plant symbionts.
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Affiliation(s)
- Pierre Gladieux
- UMR BGPI, INRA, CIRAD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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Huang X, Sun M, Lu X, Li S. Serial passage through resistant and susceptible cucumber cultivars affects the virulence of Fusarium oxysporum f. sp. cucumerinum. Microbiologyopen 2019; 8:e00641. [PMID: 29797483 PMCID: PMC6391263 DOI: 10.1002/mbo3.641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/07/2018] [Accepted: 03/24/2018] [Indexed: 12/18/2022] Open
Abstract
Fusarium oxysporum f. sp. cucumerinum (Foc) is the causal pathogen of cucumber Fusarium wilt resulting in losses to cucumber production. To investigate the effects of the selective pressures of host plants on the virulence of Foc, a low virulence isolate, foc-3b, was successively inoculated on resistant and susceptible cucumber cultivars for five generations. The virulence of the original isolate diverged; virulence was significantly strengthened after serial passage on the resistant cultivar and weakened on the susceptible plants (p ˂ .05). The expression of four virulence-related genes of F. oxysporum, G-protein α subunit gene fga1, sucrose nonfermenting 1 gene snf1, F-box protein gene frp1, and Class V chitin synthase gene chsV, was quantified using real-time PCR. All genes were significantly upregulated after serial passage on the resistant cultivar, compared to the original strain, and the expression of snf1 was downregulated in strains re-isolated from the susceptible plants (p ˂ .05). A significant positive correlation was found between the expression levels of gene snf1, frp1, and chsV and disease severity of cucumber Fusarium wilt, suggesting these genes may impact virulence differentiation. This study will improve the management of cucumber Fusarium wilt and provide insight into the mechanisms underlying virulence of F. oxysporum.
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Affiliation(s)
- Xiaoqing Huang
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Manhong Sun
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaohong Lu
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Shidong Li
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
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Bousset L, Sprague SJ, Thrall PH, Barrett LG. Spatio-temporal connectivity and host resistance influence evolutionary and epidemiological dynamics of the canola pathogen Leptosphaeria maculans. Evol Appl 2018; 11:1354-1370. [PMID: 30151045 PMCID: PMC6099830 DOI: 10.1111/eva.12630] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/07/2018] [Indexed: 11/27/2022] Open
Abstract
Genetic, physiological and physical homogenization of agricultural landscapes creates ideal environments for plant pathogens to proliferate and rapidly evolve. Thus, a critical challenge in plant pathology and epidemiology is to design durable and effective strategies to protect cropping systems from damage caused by pathogens. Theoretical studies suggest that spatio-temporal variation in the diversity and distribution of resistant hosts across agricultural landscapes may have strong effects on the epidemiology and evolutionary potential of crop pathogens. However, we lack empirical tests of spatio-temporal deployment of host resistance to pathogens can be best used to manage disease epidemics and disrupt pathogen evolutionary dynamics in real-world systems. In a field experiment, we simulated how differences in Brassica napus resistance deployment strategies and landscape connectivity influence epidemic severity and Leptosphaeria maculans pathogen population composition. Host plant resistance, spatio-temporal connectivity [stubble loads], and genetic connectivity of the inoculum source [composition of canola stubble mixtures] jointly impacted epidemiology (disease severity) and pathogen evolution (population composition). Changes in population composition were consistent with directional selection for the ability to infect the host (infectivity), leading to changes in pathotype (multilocus phenotypes) and infectivity frequencies. We repeatedly observed decreases in the frequency of unnecessary infectivity, suggesting that carrying multiple infectivity genes is costly for the pathogen. From an applied perspective, our results indicate that varying resistance genes in space and time can be used to help control disease, even when resistance has already been overcome. Furthermore, our approach extends our ability to test not only for the efficacy of host varieties in a given year, but also for durability over multiple cropping seasons, given variation in the combination of resistance genes deployed.
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Affiliation(s)
- Lydia Bousset
- CSIRO Agriculture & FoodCanberraACTAustralia
- UMR1349 IGEPPINRALe RheuFrance
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Zhang X, Farah N, Rolston L, Ericsson DJ, Catanzariti A, Bernoux M, Ve T, Bendak K, Chen C, Mackay JP, Lawrence GJ, Hardham A, Ellis JG, Williams SJ, Dodds PN, Jones DA, Kobe B. Crystal structure of the Melampsora lini effector AvrP reveals insights into a possible nuclear function and recognition by the flax disease resistance protein P. MOLECULAR PLANT PATHOLOGY 2018; 19:1196-1209. [PMID: 28817232 PMCID: PMC6638141 DOI: 10.1111/mpp.12597] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 05/23/2023]
Abstract
The effector protein AvrP is secreted by the flax rust fungal pathogen (Melampsora lini) and recognized specifically by the flax (Linum usitatissimum) P disease resistance protein, leading to effector-triggered immunity. To investigate the biological function of this effector and the mechanisms of specific recognition by the P resistance protein, we determined the crystal structure of AvrP. The structure reveals an elongated zinc-finger-like structure with a novel interleaved zinc-binding topology. The residues responsible for zinc binding are conserved in AvrP effector variants and mutations of these motifs result in a loss of P-mediated recognition. The first zinc-coordinating region of the structure displays a positively charged surface and shows some limited similarities to nucleic acid-binding and chromatin-associated proteins. We show that the majority of the AvrP protein accumulates in the plant nucleus when transiently expressed in Nicotiana benthamiana cells, suggesting a nuclear pathogenic function. Polymorphic residues in AvrP and its allelic variants map to the protein surface and could be associated with differences in recognition specificity. Several point mutations of residues on the non-conserved surface patch result in a loss of recognition by P, suggesting that these residues are required for recognition.
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Affiliation(s)
- Xiaoxiao Zhang
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Nadya Farah
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Laura Rolston
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Daniel J. Ericsson
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Australian Synchrotron, Macromolecular crystallographyClaytonVictoria 3168Australia
| | - Ann‐Maree Catanzariti
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Thomas Ve
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Institute for Glycomics, Griffith UniversitySouthportQueensland 4222Australia
| | - Katerina Bendak
- School of Molecular BioscienceUniversity of SydneySydneyNew South Wales 2006Australia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Joel P. Mackay
- School of Molecular BioscienceUniversity of SydneySydneyNew South Wales 2006Australia
| | - Gregory J. Lawrence
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Adrienne Hardham
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Jeffrey G. Ellis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Simon J. Williams
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - David A. Jones
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
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Schirrmann MK, Zoller S, Croll D, Stukenbrock EH, Leuchtmann A, Fior S. Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization. Mol Ecol 2018; 27:3070-3086. [PMID: 29633410 DOI: 10.1111/mec.14585] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022]
Abstract
Host specialization is a key process in ecological divergence and speciation of plant-associated fungi. The underlying determinants of host specialization are generally poorly understood, especially in endophytes, which constitute one of the most abundant components of the plant microbiome. We addressed the genetic basis of host specialization in two sympatric subspecies of grass-endophytic fungi from the Epichloë typhina complex: subsp. typhina and clarkii. The life cycle of these fungi entails unrestricted dispersal of gametes and sexual reproduction before infection of a new host, implying that the host imposes a selective barrier on viability of the progeny. We aimed to detect genes under divergent selection between subspecies, experiencing restricted gene flow due to adaptation to different hosts. Using pooled whole-genome sequencing data, we combined FST and DXY population statistics in genome scans and detected 57 outlier genes showing strong differentiation between the two subspecies. Genomewide analyses of nucleotide diversity (π), Tajima's D and dN/dS ratios indicated that these genes have evolved under positive selection. Genes encoding secreted proteins were enriched among the genes showing evidence of positive selection, suggesting that molecular plant-fungus interactions are strong drivers of endophyte divergence. We focused on five genes encoding secreted proteins, which were further sequenced in 28 additional isolates collected across Europe to assess genetic variation in a larger sample size. Signature of positive selection in these isolates and putative identification of pathogenic function supports our findings that these genes represent strong candidates for host specialization determinants in Epichloë endophytes. Our results highlight the role of secreted proteins as key determinants of host specialization.
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Affiliation(s)
- Melanie K Schirrmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland.,Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Adrian Leuchtmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
| | - Simone Fior
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
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McNally KE, Menardo F, Lüthi L, Praz CR, Müller MC, Kunz L, Ben‐David R, Chandrasekhar K, Dinoor A, Cowger C, Meyers E, Xue M, Zeng F, Gong S, Yu D, Bourras S, Keller B. Distinct domains of the AVRPM3 A2/F2 avirulence protein from wheat powdery mildew are involved in immune receptor recognition and putative effector function. THE NEW PHYTOLOGIST 2018; 218:681-695. [PMID: 29453934 PMCID: PMC6175116 DOI: 10.1111/nph.15026] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/05/2018] [Indexed: 05/22/2023]
Abstract
Recognition of the AVRPM3A2/F2 avirulence protein from powdery mildew by the wheat PM3A/F immune receptor induces a hypersensitive response after co-expression in Nicotiana benthamiana. The molecular determinants of this interaction and how they shape natural AvrPm3a2/f2 allelic diversity are unknown. We sequenced the AvrPm3a2/f2 gene in a worldwide collection of 272 mildew isolates. Using the natural polymorphisms of AvrPm3a2/f2 as well as sequence information from related gene family members, we tested 85 single-residue-altered AVRPM3A2/F2 variants with PM3A, PM3F and PM3FL456P/Y458H (modified for improved signaling) in Nicotiana benthamiana for effects on recognition. An intact AvrPm3a2/f2 gene was found in all analyzed isolates and the protein variant recognized by PM3A/F occurred globally at high frequencies. Single-residue alterations in AVRPM3A2/F2 mostly disrupted, but occasionally enhanced, the recognition response by PM3A, PM3F and PM3FL456P/Y458H . Residues enhancing hypersensitive responses constituted a protein domain separate from both naturally occurring polymorphisms and positively selected residues of the gene family. These results demonstrate the utility of using gene family sequence diversity to screen residues for their role in recognition. This approach identified a putative interaction surface in AVRPM3A2/F2 not polymorphic in natural alleles. We conclude that molecular mechanisms besides recognition drive AvrPm3a2/f2 diversification.
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Affiliation(s)
- Kaitlin Elyse McNally
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Linda Lüthi
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Coraline Rosalie Praz
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Lukas Kunz
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Roi Ben‐David
- Institute of Plant ScienceARO‐Volcani Center50250Bet DaganIsrael
| | - Kottakota Chandrasekhar
- Department of Plant Pathology and MicrobiologyThe Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Amos Dinoor
- Department of Plant Pathology and MicrobiologyThe Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Christina Cowger
- United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS)North Carolina State UniversityRaleighNC27695USA
- Department of Plant PathologyNorth Carolina State UniversityRaleighNC27695USA
| | - Emily Meyers
- Department of Plant PathologyNorth Carolina State UniversityRaleighNC27695USA
| | - Mingfeng Xue
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
| | - Fangsong Zeng
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
| | - Shuangjun Gong
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
- College of Life ScienceWuhan University430072WuhanChina
| | - Dazhao Yu
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
- College of Life ScienceWuhan University430072WuhanChina
| | - Salim Bourras
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Beat Keller
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
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32
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Möller M, Stukenbrock EH. Evolution and genome architecture in fungal plant pathogens. Nat Rev Microbiol 2017; 15:756-771. [DOI: 10.1038/nrmicro.2017.76] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Cooper B, Campbell KB. Protection Against Common Bean Rust Conferred by a Gene-Silencing Method. PHYTOPATHOLOGY 2017; 107:920-927. [PMID: 28437139 DOI: 10.1094/phyto-03-17-0095-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rust disease of the dry bean plant, Phaseolus vulgaris, is caused by the fungus Uromyces appendiculatus. The fungus acquires its nutrients and energy from bean leaves using a specialized cell structure, the haustorium, through which it secretes effector proteins that contribute to pathogenicity by defeating the plant immune system. Candidate effectors have been identified by DNA sequencing and motif analysis, and some candidates have been observed in infected leaves by mass spectrometry. To assess their roles in pathogenicity, we have inserted small fragments of genes for five candidates into Bean pod mottle virus. Plants were infected with recombinant virus and then challenged with U. appendiculatus. Virus-infected plants expressing gene fragments for four of five candidate effectors accumulated lower amounts of rust and had dramatically less rust disease. By contrast, controls that included a fungal gene fragment for a septin protein not expressed in the haustorium died from a synergistic reaction between the virus and the fungus. The results imply that RNA generated in the plant moved across the fungal haustorium to silence effector genes important to fungal pathogenicity. This study shows that four bean rust fungal genes encode pathogenicity determinants and that the expression of fungal RNA in the plant can be an effective method for protecting bean plants from rust.
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Affiliation(s)
- Bret Cooper
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
| | - Kimberly B Campbell
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
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Li Y, Yin M, Wu Q, McManus DP, Blair D, Li H, Xu B, Mo X, Feng Z, Hu W. Genetic diversity and selection of three nuclear genes in Schistosoma japonicum populations. Parasit Vectors 2017; 10:87. [PMID: 28212676 PMCID: PMC5316221 DOI: 10.1186/s13071-017-2033-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The blood fluke, Schistosoma japonicum still causes severe disease in China, the Philippines and Indonesia. Although there have been some studies the molecular epidemiology of this persistent and harmful parasite, few have explored the possibility and implications of selection in S. japonicum populations. METHODS We analyzed diversity and looked for evidence of selection at three nuclear genes (SjIpp2, SjFabp and SjT22.6) in 13 S. japonicum populations. RESULTS SjT22.6 was found to exhibit high nucleotide diversity and was under positive selection in the mountainous region of mainland China. As a tegumental protein, its secondary and tertiary structure differed between S. japonicum strains from the mountainous and lakes regions. In contrast, SjIpp2 and SjFabp had relatively low levels of nucleotide diversity and did not show significant departure from neutrality. CONCLUSIONS As a tegument-associated antigen-encoding gene of S. japonicum, SjT22.6 has high nucleotide diversity and appears to be under positive selection in the mountainous region of mainland China.
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Affiliation(s)
- Yaqi Li
- School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Mingbo Yin
- School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Qunfeng Wu
- School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Donald P. McManus
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, QLD 4029 Australia
| | - David Blair
- College of Science and Engineering, James Cook University, Townsville, QLD 4811 Australia
| | - Hongyan Li
- School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025 China
| | - Xiaojin Mo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025 China
| | - Zheng Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025 China
| | - Wei Hu
- School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025 China
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Maia T, Badel JL, Marin‐Ramirez G, Rocha CDM, Fernandes MB, da Silva JCF, de Azevedo‐Junior GM, Brommonschenkel SH. The Hemileia vastatrix effector HvEC-016 suppresses bacterial blight symptoms in coffee genotypes with the S H 1 rust resistance gene. THE NEW PHYTOLOGIST 2017; 213:1315-1329. [PMID: 27918080 PMCID: PMC6079635 DOI: 10.1111/nph.14334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/16/2016] [Indexed: 05/03/2023]
Abstract
A number of genes that confer resistance to coffee leaf rust (SH 1-SH 9) have been identified within the genus Coffea, but despite many years of research on this pathosystem, the complementary avirulence genes of Hemileia vastatrix have not been reported. After identification of H. vastatrix effector candidate genes (HvECs) expressed at different stages of its lifecycle, we established an assay to characterize HvEC proteins by delivering them into coffee cells via the type-three secretion system (T3SS) of Pseudomonas syringae pv. garcae (Psgc). Employing a calmodulin-dependent adenylate cyclase assay, we demonstrate that Psgc recognizes a heterologous P. syringae T3SS secretion signal which enables us to translocate HvECs into the cytoplasm of coffee cells. Using this Psgc-adapted effector detector vector (EDV) system, we found that HvEC-016 suppresses the growth of Psgc on coffee genotypes with the SH 1 resistance gene. Suppression of bacterial blight symptoms in SH 1 plants was associated with reduced bacterial multiplication. By contrast, HvEC-016 enhanced bacterial multiplication in SH 1-lacking plants. Our findings suggest that HvEC-016 may be recognized by the plant immune system in a SH 1-dependent manner. Thus, our experimental approach is an effective tool for the characterization of effector/avirulence proteins of this important pathogen.
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Affiliation(s)
- Thiago Maia
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Jorge L. Badel
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Gustavo Marin‐Ramirez
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Cynthia de M. Rocha
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Michelle B. Fernandes
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - José C. F. da Silva
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Gilson M. de Azevedo‐Junior
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Sérgio H. Brommonschenkel
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
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Zhang X, Nguyen N, Breen S, Outram MA, Dodds PN, Kobe B, Solomon PS, Williams SJ. Production of small cysteine-rich effector proteins in Escherichia coli for structural and functional studies. MOLECULAR PLANT PATHOLOGY 2017; 18:141-151. [PMID: 26915457 PMCID: PMC6638209 DOI: 10.1111/mpp.12385] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 02/22/2016] [Accepted: 02/22/2016] [Indexed: 05/22/2023]
Abstract
Although the lifestyles and infection strategies of plant pathogens are diverse, a prevailing feature is the use of an arsenal of secreted proteins, known as effectors, which aid in microbial infection. In the case of eukaryotic filamentous pathogens, such as fungi and oomycetes, effector proteins are typically dissimilar, at the protein sequence level, to known protein families and functional domains. Consequently, we currently have a limited understanding of how fungal and oomycete effectors promote disease. Protein biochemistry and structural biology are two methods that can contribute greatly to the understanding of protein function. Both techniques are dependent on obtaining proteins that are pure and functional, and generally require the use of heterologous recombinant protein expression systems. Here, we present a general scheme and methodology for the production and characterization of small cysteine-rich (SCR) effectors utilizing Escherichia coli expression systems. Using this approach, we successfully produced cysteine-rich effectors derived from the biotrophic fungal pathogen Melampsora lini and the necrotrophic fungal pathogen Parastagonospora nodorum. Access to functional recombinant proteins facilitated crystallization and functional experiments. These results are discussed in the context of a general workflow that may serve as a template for others interested in understanding the function of SCR effector(s) from their plant pathogen(s) of interest.
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Affiliation(s)
- Xiaoxiao Zhang
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research CentreUniversity of QueenslandBrisbaneQld4072Australia
| | - Neal Nguyen
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research CentreUniversity of QueenslandBrisbaneQld4072Australia
| | - Susan Breen
- Research School of BiologyThe Australian National UniversityCanberraACT 0200Australia
| | - Megan A. Outram
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research CentreUniversity of QueenslandBrisbaneQld4072Australia
| | | | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research CentreUniversity of QueenslandBrisbaneQld4072Australia
| | - Peter S. Solomon
- Research School of BiologyThe Australian National UniversityCanberraACT 0200Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research CentreUniversity of QueenslandBrisbaneQld4072Australia
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Sperschneider J, Dodds PN, Taylor JM, Duplessis S. Computational Methods for Predicting Effectors in Rust Pathogens. Methods Mol Biol 2017; 1659:73-83. [PMID: 28856642 DOI: 10.1007/978-1-4939-7249-4_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Lower costs and improved sequencing technologies have led to a large number of high-quality rust pathogen genomes and deeper characterization of gene expression profiles during early and late infection stages. However, the set of secreted proteins expressed during infection is too large for experimental investigations and contains not only effectors but also proteins that play a role in niche colonization or in fighting off competing microbes. Therefore, accurate computational prediction is essential for identifying high-priority rust effector candidates from secretomes.
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Affiliation(s)
- Jana Sperschneider
- Centre for Environmental and Life Sciences, CSIRO Agriculture and Food, Underwood Avenue, Floreat, WA, Australia.
| | - Peter N Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Jennifer M Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Sébastien Duplessis
- INRA, Unité Mixte de Recherche INRA/Université de Lorraine 1136 Interactions Arbres-Microorganismes, INRA Centre Grand Est - Nancy, Champenoux, France
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Anderson C, Khan MA, Catanzariti AM, Jack CA, Nemri A, Lawrence GJ, Upadhyaya NM, Hardham AR, Ellis JG, Dodds PN, Jones DA. Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini. BMC Genomics 2016; 17:667. [PMID: 27550217 PMCID: PMC4994203 DOI: 10.1186/s12864-016-3011-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/11/2016] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding receptors that trigger a highly effective defence response upon recognition of specific pathogen avirulence proteins. Identifying avirulence genes is crucial for understanding how virulence evolves in the field. RESULTS To facilitate avirulence gene cloning in the flax rust fungus, Melampsora lini, we constructed a high-density genetic linkage map using single nucleotide polymorphisms detected in restriction site-associated DNA sequencing (RADseq) data. The map comprises 13,412 RADseq markers in 27 linkage groups that together span 5860 cM and contain 2756 recombination bins. The marker sequences were used to anchor 68.9 % of the M. lini genome assembly onto the genetic map. The map and anchored assembly were then used to: 1) show that M. lini has a high overall meiotic recombination rate, but recombination distribution is uneven and large coldspots exist; 2) show that substantial genome rearrangements have occurred in spontaneous loss-of-avirulence mutants; and 3) identify the AvrL2 and AvrM14 avirulence genes by map-based cloning. AvrM14 is a dual-specificity avirulence gene that encodes a predicted nudix hydrolase. AvrL2 is located in the region of the M. lini genome with the lowest recombination rate and encodes a small, highly-charged proline-rich protein. CONCLUSIONS The M. lini high-density linkage map has greatly advanced our understanding of virulence mechanisms in this pathogen by providing novel insights into genome variability and enabling identification of two new avirulence genes.
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Affiliation(s)
- Claire Anderson
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | - Muhammad Adil Khan
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
- Current address: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Ann-Maree Catanzariti
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | - Cameron A. Jack
- ANU Bioinformatics Consulting Unit, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Acton, ACT 2601 Australia
| | - Adnane Nemri
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia
- Current address: KWS SAAT SE, Grimsehlstraße 31, Einbeck, 37574 Germany
| | | | | | - Adrienne R. Hardham
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | | | - Peter N. Dodds
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia
| | - David A. Jones
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
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Wu EJ, Yang LN, Zhu W, Chen XM, Shang LP, Zhan J. Diverse mechanisms shape the evolution of virulence factors in the potato late blight pathogen Phytophthora infestans sampled from China. Sci Rep 2016; 6:26182. [PMID: 27193142 PMCID: PMC4872137 DOI: 10.1038/srep26182] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/27/2016] [Indexed: 01/23/2023] Open
Abstract
Evolution of virulence in plant pathogens is still poorly understood but the knowledge is important for the effective use of plant resistance and sustainable disease management. Spatial population dynamics of virulence, race and SSR markers in 140 genotypes sampled from seven geographic locations in China were compared to infer the mechanisms driving the evolution of virulence in Phytophthora infestans (P. infestans). All virulence types and a full spectrum of race complexity, ranging from the race able to infect the universally susceptible cultivar only to all differentials, were detected. Eight and two virulence factors were under diversifying and constraining selection respectively while no natural selection was detected in one of the virulence types. Further analyses revealed excesses in simple and complex races but deficiency in intermediate race and negative associations of annual mean temperature at the site from which pathogen isolates were collected with frequency of virulence to differentials and race complexity in the pathogen populations. These results suggest that host selection may interact with other factors such as climatic conditions in determining the evolutionary trajectory of virulence and race structure in P. infestans and global warming may slow down the emergence of new virulence in the pathogen.
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Affiliation(s)
- E-Jiao Wu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China
| | - Li-Na Yang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China
| | - Wen Zhu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China
| | - Xiao-Mei Chen
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China
| | - Li-Ping Shang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China
| | - Jiasui Zhan
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China
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40
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Cooper B, Campbell KB, Beard HS, Garrett WM, Islam N. Putative Rust Fungal Effector Proteins in Infected Bean and Soybean Leaves. PHYTOPATHOLOGY 2016; 106:491-9. [PMID: 26780434 DOI: 10.1094/phyto-11-15-0310-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The plant-pathogenic fungi Uromyces appendiculatus and Phakopsora pachyrhizi cause debilitating rust diseases on common bean and soybean. These rust fungi secrete effector proteins that allow them to infect plants, but their effector repertoires are not understood. The discovery of rust fungus effectors may eventually help guide decisions and actions that mitigate crop production loss. Therefore, we used mass spectrometry to identify thousands of proteins in infected beans and soybeans and in germinated fungal spores. The comparative analysis between the two helped differentiate a set of 24 U. appendiculatus proteins targeted for secretion that were specifically found in infected beans and a set of 34 U. appendiculatus proteins targeted for secretion that were found in germinated spores and infected beans. The proteins specific to infected beans included family 26 and family 76 glycoside hydrolases that may contribute to degrading plant cell walls. There were also several types of proteins with structural motifs that may aid in stabilizing the specialized fungal haustorium cell that interfaces the plant cell membrane during infection. There were 16 P. pachyrhizi proteins targeted for secretion that were found in infected soybeans, and many of these proteins resembled the U. appendiculatus proteins found in infected beans, which implies that these proteins are important to rust fungal pathology in general. This data set provides insight to the biochemical mechanisms that rust fungi use to overcome plant immune systems and to parasitize cells.
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Affiliation(s)
- Bret Cooper
- First, second, and third authors: Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD 20705; fourth author: Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, MD 20705; and fifth author: Department of Nutrition and Food Science, University of Maryland, College Park 20742
| | - Kimberly B Campbell
- First, second, and third authors: Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD 20705; fourth author: Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, MD 20705; and fifth author: Department of Nutrition and Food Science, University of Maryland, College Park 20742
| | - Hunter S Beard
- First, second, and third authors: Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD 20705; fourth author: Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, MD 20705; and fifth author: Department of Nutrition and Food Science, University of Maryland, College Park 20742
| | - Wesley M Garrett
- First, second, and third authors: Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD 20705; fourth author: Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, MD 20705; and fifth author: Department of Nutrition and Food Science, University of Maryland, College Park 20742
| | - Nazrul Islam
- First, second, and third authors: Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD 20705; fourth author: Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, MD 20705; and fifth author: Department of Nutrition and Food Science, University of Maryland, College Park 20742
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Kenaley SC, Hudler GW, Bergstrom GC. Detection and phylogenetic relationships of Puccinia emaculata and Uromyces graminicola (Pucciniales) on switchgrass in New York State using rDNA sequence information. Fungal Biol 2016; 120:791-806. [PMID: 27109375 DOI: 10.1016/j.funbio.2016.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Abstract
The species of rust fungi (Pucciniales) inciting disease on switchgrass (Panicum virgatum) grown in bioenergy feedstock systems across the north-central and eastern United States remain unclear. In the present study, the species number and phylogenetic relationships of rust species affecting switchgrass were examined in 2011-2013 at two sites in New York State as well as selected sites in Alabama, Iowa, Nebraska, Pennsylvania, South Dakota, and West Virginia using ribosomal RNA gene data (partial internal transcribed spacer [ITS] 1, complete 5.8 subunit [S] and ITS2, and partial 28S). Uredinial group and teliospore morphology were also utilized to delimit taxa in collection years 2012 and 2013. Maximum likelihood, maximum parsimony, and Bayesian analyses demonstrated two monophyletic clades. Clade I consisted of Puccinia emaculata and included the majority of single-sorus samples across sites, whereas, Clade II included multiple samples from Iowa, Nebraska, and South Dakota. Single-telial samples for Clade I possessed only two-celled teliospores while Clade II samples possessed only one-celled teliospores, and hence, were readily diagnosed morphologically to P. emaculata and Uromyces graminicola, respectively. No U. graminicola sequences exist in GenBank to compare with our Clade II samples; however, based on teliospore morphology, the identity of Clade II taxa is U. graminicola.
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Affiliation(s)
- Shawn C Kenaley
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853-5904, USA.
| | - George W Hudler
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853-5904, USA
| | - Gary C Bergstrom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853-5904, USA
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Jan P, Gracianne C, Fournet S, Olivier E, Arnaud J, Porte C, Bardou‐Valette S, Denis M, Petit EJ. Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 1. Insights from the estimation of effective population sizes. Evol Appl 2016; 9:489-501. [PMID: 26989440 PMCID: PMC4778111 DOI: 10.1111/eva.12352] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 12/14/2015] [Indexed: 12/05/2022] Open
Abstract
The sustainability of modern agriculture relies on strategies that can control the ability of pathogens to overcome chemicals or genetic resistances through natural selection. This evolutionary potential, which depends partly on effective population size (N e ), is greatly influenced by human activities. In this context, wild pathogen populations can provide valuable information for assessing the long-term risk associated with crop pests. In this study, we estimated the effective population size of the beet cyst nematode, Heterodera schachtii, by sampling 34 populations infecting the sea beet Beta vulgaris spp. maritima twice within a one-year period. Only 20 populations produced enough generations to analyze the variation in allele frequencies, with the remaining populations showing a high mortality rate of the host plant after only 1 year. The 20 analyzed populations showed surprisingly low effective population sizes, with most having N e close to 85 individuals. We attribute these low values to the variation in population size through time, systematic inbreeding, and unbalanced sex-ratios. Our results suggest that H. schachtii has low evolutionary potential in natural environments. Pest control strategies in which populations on crops mimic wild populations may help prevent parasite adaptation to host resistance.
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Affiliation(s)
- Pierre‐Loup Jan
- INRAUMR1349 IGEPPF‐35653Le Rheu CedexFrance
- INRAUMR985 ESEF‐35042Rennes CedexFrance
| | | | | | | | - Jean‐François Arnaud
- UMR CNRS 8198 Évolution, Écologie et PaléontologieUniversité Lille 1 – Sciences et Technologies59655Villeneuve d'Ascq CedexFrance
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Figueroa M, Upadhyaya NM, Sperschneider J, Park RF, Szabo LJ, Steffenson B, Ellis JG, Dodds PN. Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici. FRONTIERS IN PLANT SCIENCE 2016; 7:205. [PMID: 26941766 PMCID: PMC4764693 DOI: 10.3389/fpls.2016.00205] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/06/2016] [Indexed: 05/03/2023]
Abstract
The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes.
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Affiliation(s)
- Melania Figueroa
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
| | - Narayana M. Upadhyaya
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Jana Sperschneider
- Agriculture, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research OrganisationPerth, WA, Australia
| | - Robert F. Park
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Les J. Szabo
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research ServiceSt. Paul, MN, USA
| | - Brian Steffenson
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
| | - Jeff G. Ellis
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Peter N. Dodds
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
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Mbengue M, Navaud O, Peyraud R, Barascud M, Badet T, Vincent R, Barbacci A, Raffaele S. Emerging Trends in Molecular Interactions between Plants and the Broad Host Range Fungal Pathogens Botrytis cinerea and Sclerotinia sclerotiorum. FRONTIERS IN PLANT SCIENCE 2016; 7:422. [PMID: 27066056 PMCID: PMC4814483 DOI: 10.3389/fpls.2016.00422] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/18/2016] [Indexed: 05/08/2023]
Abstract
Fungal plant pathogens are major threats to food security worldwide. Sclerotinia sclerotiorum and Botrytis cinerea are closely related Ascomycete plant pathogens causing mold diseases on hundreds of plant species. There is no genetic source of complete plant resistance to these broad host range pathogens known to date. Instead, natural plant populations show a continuum of resistance levels controlled by multiple genes, a phenotype designated as quantitative disease resistance. Little is known about the molecular mechanisms controlling the interaction between plants and S. sclerotiorum and B. cinerea but significant advances were made on this topic in the last years. This minireview highlights a selection of nine themes that emerged in recent research reports on the molecular bases of plant-S. sclerotiorum and plant-B. cinerea interactions. On the fungal side, this includes progress on understanding the role of oxalic acid, on the study of fungal small secreted proteins. Next, we discuss the exchanges of small RNA between organisms and the control of cell death in plant and fungi during pathogenic interactions. Finally on the plant side, we highlight defense priming by mechanical signals, the characterization of plant Receptor-like proteins and the hormone abscisic acid in the response to B. cinerea and S. sclerotiorum, the role of plant general transcription machinery and plant small bioactive peptides. These represent nine trends we selected as remarkable in our understanding of fungal molecules causing disease and plant mechanisms associated with disease resistance to two devastating broad host range fungi.
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Bourras S, McNally KE, Müller MC, Wicker T, Keller B. Avirulence Genes in Cereal Powdery Mildews: The Gene-for-Gene Hypothesis 2.0. FRONTIERS IN PLANT SCIENCE 2016; 7:241. [PMID: 26973683 PMCID: PMC4771761 DOI: 10.3389/fpls.2016.00241] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/12/2016] [Indexed: 05/22/2023]
Abstract
The gene-for-gene hypothesis states that for each gene controlling resistance in the host, there is a corresponding, specific gene controlling avirulence in the pathogen. Allelic series of the cereal mildew resistance genes Pm3 and Mla provide an excellent system for genetic and molecular analysis of resistance specificity. Despite this opportunity for molecular research, avirulence genes in mildews remain underexplored. Earlier work in barley powdery mildew (B.g. hordei) has shown that the reaction to some Mla resistance alleles is controlled by multiple genes. Similarly, several genes are involved in the specific interaction of wheat mildew (B.g. tritici) with the Pm3 allelic series. We found that two mildew genes control avirulence on Pm3f: one gene is involved in recognition by the resistance protein as demonstrated by functional studies in wheat and the heterologous host Nicotiana benthamiana. A second gene is a suppressor, and resistance is only observed in mildew genotypes combining the inactive suppressor and the recognized Avr. We propose that such suppressor/avirulence gene combinations provide the basis of specificity in mildews. Depending on the particular gene combinations in a mildew race, different genes will be genetically identified as the "avirulence" gene. Additionally, the observation of two LINE retrotransposon-encoded avirulence genes in B.g. hordei further suggests that the control of avirulence in mildew is more complex than a canonical gene-for-gene interaction. To fully understand the mildew-cereal interactions, more knowledge on avirulence determinants is needed and we propose ways how this can be achieved based on recent advances in the field.
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Louis B, Waikhom SD, Jose RC, Goyari S, Talukdar NC, Roy P. Cochliobolus lunatus colonizes potato by adopting different invasion strategies on cultivars: New insights on temperature dependent-virulence. Microb Pathog 2015. [DOI: 10.1016/j.micpath.2015.07.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen. Genetics 2015; 201:1213-28. [PMID: 26392286 DOI: 10.1534/genetics.115.180968] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/17/2015] [Indexed: 12/30/2022] Open
Abstract
Recombination has an impact on genome evolution by maintaining chromosomal integrity, affecting the efficacy of selection, and increasing genetic variability in populations. Recombination rates are a key determinant of the coevolutionary dynamics between hosts and their pathogens. Historic recombination events created devastating new pathogens, but the impact of ongoing recombination in sexual pathogens is poorly understood. Many fungal pathogens of plants undergo regular sexual cycles, and sex is considered to be a major factor contributing to virulence. We generated a recombination map at kilobase-scale resolution for the haploid plant pathogenic fungus Zymoseptoria tritici. To account for intraspecific variation in recombination rates, we constructed genetic maps from two independent crosses. We localized a total of 10,287 crossover events in 441 progeny and found that recombination rates were highly heterogeneous within and among chromosomes. Recombination rates on large chromosomes were inversely correlated with chromosome length. Short accessory chromosomes often lacked evidence for crossovers between parental chromosomes. Recombination was concentrated in narrow hotspots that were preferentially located close to telomeres. Hotspots were only partially conserved between the two crosses, suggesting that hotspots are short-lived and may vary according to genomic background. Genes located in hotspot regions were enriched in genes encoding secreted proteins. Population resequencing showed that chromosomal regions with high recombination rates were strongly correlated with regions of low linkage disequilibrium. Hence, genes in pathogen recombination hotspots are likely to evolve faster in natural populations and may represent a greater threat to the host.
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Sperschneider J, Gardiner DM, Thatcher LF, Lyons R, Singh KB, Manners JM, Taylor JM. Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity. Genome Biol Evol 2015; 7:1613-27. [PMID: 25994930 PMCID: PMC4494044 DOI: 10.1093/gbe/evv092] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pathogens and hosts are in an ongoing arms race and genes involved in host–pathogen interactions are likely to undergo diversifying selection. Fusarium plant pathogens have evolved diverse infection strategies, but how they interact with their hosts in the biotrophic infection stage remains puzzling. To address this, we analyzed the genomes of three Fusarium plant pathogens for genes that are under diversifying selection. We found a two-speed genome structure both on the chromosome and gene group level. Diversifying selection acts strongly on the dispensable chromosomes in Fusarium oxysporum f. sp. lycopersici and on distinct core chromosome regions in Fusarium graminearum, all of which have associations with virulence. Members of two gene groups evolve rapidly, namely those that encode proteins with an N-terminal [SG]-P-C-[KR]-P sequence motif and proteins that are conserved predominantly in pathogens. Specifically, 29 F. graminearum genes are rapidly evolving, in planta induced and encode secreted proteins, strongly pointing toward effector function. In summary, diversifying selection in Fusarium is strongly reflected as genomic footprints and can be used to predict a small gene set likely to be involved in host–pathogen interactions for experimental verification.
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Affiliation(s)
- Jana Sperschneider
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia
| | - Donald M Gardiner
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Louise F Thatcher
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia
| | - Rebecca Lyons
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Karam B Singh
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
| | - John M Manners
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
| | - Jennifer M Taylor
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
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Laine AL, Burdon JJ, Nemri A, Thrall PH. Host ecotype generates evolutionary and epidemiological divergence across a pathogen metapopulation. Proc Biol Sci 2015; 281:rspb.2014.0522. [PMID: 24870042 DOI: 10.1098/rspb.2014.0522] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The extent and speed at which pathogens adapt to host resistance varies considerably. This presents a challenge for predicting when--and where--pathogen evolution may occur. While gene flow and spatially heterogeneous environments are recognized to be critical for the evolutionary potential of pathogen populations, we lack an understanding of how the two jointly shape coevolutionary trajectories between hosts and pathogens. The rust pathogen Melampsora lini infects two ecotypes of its host plant Linum marginale that occur in close proximity yet in distinct populations and habitats. In this study, we found that within-population epidemics were different between the two habitats. We then tested for pathogen local adaptation at host population and ecotype level in a reciprocal inoculation study. Even after controlling for the effect of spatial structure on infection outcome, we found strong evidence of pathogen adaptation at the host ecotype level. Moreover, sequence analysis of two pathogen infectivity loci revealed strong genetic differentiation by host ecotype but not by distance. Hence, environmental variation can be a key determinant of pathogen population genetic structure and coevolutionary dynamics and can generate strong asymmetry in infection risks through space.
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Affiliation(s)
- Anna-Liisa Laine
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki 00014, Finland
| | - Jeremy J Burdon
- CSIRO Plant Industry, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - Adnane Nemri
- CSIRO Plant Industry, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - Peter H Thrall
- CSIRO Plant Industry, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
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Upadhyaya NM, Garnica DP, Karaoglu H, Sperschneider J, Nemri A, Xu B, Mago R, Cuomo CA, Rathjen JP, Park RF, Ellis JG, Dodds PN. Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes. FRONTIERS IN PLANT SCIENCE 2015; 5:759. [PMID: 25620970 PMCID: PMC4288056 DOI: 10.3389/fpls.2014.00759] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 12/09/2014] [Indexed: 05/03/2023]
Abstract
The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.
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Affiliation(s)
- Narayana M. Upadhyaya
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Diana P. Garnica
- Research School of Biology, Australian National UniversityCanberra, ACT, Australia
| | - Haydar Karaoglu
- Plant Breeding Institute, Faculty of Agriculture and Environment, The University of SydneyNarellan, NSW, Australia
| | - Jana Sperschneider
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Adnane Nemri
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Bo Xu
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Rohit Mago
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Christina A. Cuomo
- Genome Sequencing and Analysis Program, Broad Institute of MIT and HarvardCambridge, MA, USA
| | - John P. Rathjen
- Research School of Biology, Australian National UniversityCanberra, ACT, Australia
| | - Robert F. Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, The University of SydneyNarellan, NSW, Australia
| | - Jeffrey G. Ellis
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Peter N. Dodds
- Agriculture Flagship, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
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